Evolution Can Be More Random Than You Think

Charles Darwin’s Origin of Species postulated that evolution takes a directed approach toward increasing fitness. A recent discovery suggests that evolution doesn’t always need to have a direction. Dr. Matthew Pennell’s findings suggest that evolution on a chromosomal level can have a high degree of randomness.

Dr. Matthew Pennell, an evolutionary biologist specializing in Computational Biology at the University of British Columbia, recently wrote a paper that gives more insight on evolution, entitled Y-Fuse? Sex Chromosome Fusions in Fishes and ReptilesIn this paper, Dr. Pennell uses software and algorithms to determine the factors that drive sex chromosome fusions. Unlike traditional biologists, Dr. Pennell does all of his work on his MacBook instead of using pipettes and microscopes.

Source: Wikimedia Commons, Dr.Pennell uses computational approaches, such as Mathematica for his research.

Source: Wikimedia Commons, Dr.Pennell uses computational approaches, such as Mathematica for his research.

This video, courtesy of universityofbc via Youtub, introduces UBC Killam and NSERC postdoctoral fellow, Dr. Matthew Pennell and talks about his research

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“The simple fact that Y autosome fusions are way more common than W or X or Z, suggests it’s probably just random, which is a kind of interesting and cool result that this huge thing in our genome and across all genomes is just random chance, and this random chance explanation is the most consistent with our data.”

 -Dr. Matthew Pennell

During his graduate studies, Dr.Pennel was part of a team that integrated chromosomal information of thousands of species into an electronic database called The Tree of Sex, which we describe in further detail in our podcast below.

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Now that we know randomness is involved in sex chromosome evolution another question arises: Is sex determination an absolute process? 

As we will soon see there are species, such as the Stickleback fish that change their sex determination system from XY, to ZW, to temperature controlled and so on. However, does this mean that we humans might experience such a change in the future?  

Source: Flickr Commons, Huamns have 22 pairs of autosomes and 1 pair of sex chromosome

Source: Flickr Commons, humans have 22 pairs of autosomes and 1 pair of sex chromosome

“They keep reinventing how they make males and females and this is really interesting and crazy because making males and females is the most basic thing animals do….But they keep switching around how they make males and   females, which I think is pretty cool.”

-Dr. Matthew Pennell

In addition, we were fortunate enough to have the opportunity to interview Dr. Pennell:

Before the interview with Dr. Pennell, our group had a lot of difficulty understanding the premise and messages of the paper. Dr. Pennell provided us with simple insights on the different facets of the evolution of sex chromosomes – from the creative variety of ways that nature determines sex in species, to the mechanisms which drive sex chromosome fusions. Although a lot of these concepts were hard to understand at first, the premise of the paper is very simple to understand – computational biologists often work with real world data sets (ie. “The Tree of Sex”, and try to fit their models to them to determine the relationships between the scientists’ predictions and what’s really happening. In this specific paper, Dr. Pennell and his team concluded that the different models did not relate to the given dataset and the explanation for the real data is attributed to randomness.

 

We would like to give a special thanks to Dr. Matthew Pennell for his time and explanation of his paper.
Authors: Justin Yoon, Julia He, Radu Nesiu, and Matt Golf (Group 2)

Looking deep within a cell, super resolution microscopy technique improved by researcher at UBC

What do you think is the smallest scale visible through a light microscope? Bacteria in micrometers? Guess again. The answer is thousands of times smaller. Last year, a Nobel Prize in Chemistry was awarded for the development of super-resolved fluorescence microscopy, which brought the imaging scale down to nanometers (billions of times smaller than a meter). Recently, Reza Tafteh, a PhD candidate from the University of British Columbia further improved on this technique. The specific version of super resolved microscopy Reza improved on is called single-molecule localization microscopy (SMLM), and it allows scientists to image deeper into a target cell with greater accuracy. An interview with Reza is available in this podcast: 

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The computer system used to operate Reza’s microscope, photo credits: Ivan Lan, Reza Tafteh

As Reza explained in the podcast, SMLM achieves high resolution through image reconstruction. Imagine looking into a traditional microscope like looking down on the city of Vancouver at night from an airplane above. It is hard to tell the contour of the city with the limited lighting. Using fluorescence on the target sample is like turning on the building lights in the city, allowing us to observe things that aren’t normally visible under the moonlight. Now imagine that these lights are constantly on and extremely bright. If the location of the lights are too close together, many of them may seem blended with each other. This makes it harder to tell apart (or resolve) smaller structures such as narrow streets from one another; which in this case is like trying to resolve narrow structures within cells. SMLM reduces this effect by turning the lights on and off at different times for different parts of the city, which you can find more details in the podcast and the video.

However, the traditional SMLM technique isn’t perfect. Alongside major limitations in stability mentioned in the podcast, another major limitation is the distortion of an image caused by changing refractive indices through several different media, just like a pen appearing bent when inserted into a cup of water. Refractive indices varies from the cover-slip to the media (the substance the cell is placed in for imaging), and from the media to the cell.

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Refractive Index difference causing image refraction. Source:Flicker Commons, Author: Mohammad Tajer

Reza Tafteh has improved on both of these limitations. His approach can produce stabilized images with reduced distortion when imaging deep into samples. Here is a video of him demonstrating his stabilization technique.
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Reza is now trying to push the limits of SMLM even further, he sets his eyes on improving the technique’s inability to image live cells, while continuing to increase the resolution and clarity of microscopy images. It is exciting to think that specific cellular structures such as heart cell calcium receptors can be observed in unprecedented detail. It is not hard to imagine the many biological fields that can benefit from this microscopy technique. Reza’s improvement on SMLM  can potentially lead to better understanding of molecular biology, which may one day lead to new treatments for diseases such as central core disease.

Music and sound material used in podcast:

A sincere thank you to Reza Tafteh for participating in this project.

By: Group 3, Brian Cheng, Esther Lo, Ivan Lan, Sainan (Stephanie) Liu

First Quantum Code Written – Implications for the Future?

quantumcomputing

Source: Flickr Commons, Charles Opper

November 17, 2015 – about 6 hours before the writing of this post – may be an important day for future generations to remember. Just 6 hours ago, University of New South Wales in Australia has released a press release that the first lines of quantum code has been written. What is quantum computing and why should anyone care?

It’s a very different concept from modern computing – which uses the typical binary system consisting 0’s and 1’s to represent data in a single unit called a bit. Quantum computing opens up many more possibilities than just 0’s and 1’s in a single unit. It can hold double the amount of states where 0-1 and 1-0 can also exist at the same time in a single unit.

Basically, the different between normal computing and quantum computing is similar to trying to send an SOS message using morse code versus texting. Using morse code, you’d have to write nine units of information to get the message across: … — … in such fashion. Using text, you would only have to type “SOS”, 3 units of information to call for help.

This means that once this technology is better understood and as more complex code for this system can be written and computed, it will be possible to store information in exponentially smaller files and compute faster. Check out the video below about quantum computing by user Veritasium on Youtube if you want to find out more about it.

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Researchers at the Google funded artificial intelligence lab at NASA believe that quantum computing could be the key to having enough processing power and efficiency, along with data efficiency to achieve artificial intelligence. I am not so sure if that is something that I would want in my life time. Call me paranoid but it would seem wise to assume that an intelligent entity would learn to put its own needs before any other being’s.

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Source: Flickr commons, Magdalena Ladrón de Guevara

Having said that, I think the benefits of quantum computing and coding, once masterd by engineers and scientists, will be a leap forward in technology. With the potential of exponentially faster processing power, we could expect next-generation iPads to outperform today’s supercomputers. Think of the possibilities!

By Justin Yoon

The CRISPRs Fever

You may remember from biology textbook that we can edit genetic material using restriction enzymes, a DNA-cutting protein structure. Using this we can learn about gene functionalities, search for disease treatments or increase yields of crops. Controversially, it also made unnatural creations possible. However, different gene targets require different enzyme structures, just like to open different doors you need different keys, and making these “keys” turns out to be complicated, expensive and time-consuming, which might have kept most of the “fantasies”, such as “super human” or other wired things, away from reality for now for better or worse.

by PuraVida_Fotografie from Google Image "genetic mutation" Labeled for reuse

by PuraVida_Fotografie from Google Image search “genetic mutation”, labeled for reuse.

However, what if all the “doors” also have the same type of “digital locks”, and all you need to change is the password? CRISPRs (clustered regularly interspaced short palindromic repeats) turns out to be this “lock”. It contains repeated sequences sandwiched with spacers (unique genetic information) in between. The spacers are external virus genes kept in bacterias and served as the “criminal records” so that when invasion happens again, the bacteria can send an “army” of gene-cutting enzymes, called Cas9, to cut the recognized viruses’ DNA apart.

"Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA" by Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki - Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA http://dx.doi.org/10.1016/j.cell.2014.02.001. Licensed under CC BY-SA 3.0 via Commons

“Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA” by Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki – Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA http://dx.doi.org/10.1016/j.cell.2014.02.001. Licensed under CC BY-SA 3.0 via Commons

In 2012, scientists have proven that instead of making restriction enzymes for different genes, we can simply replace these “criminal records” and use the same Cas9 “armies” to cut desired genes with much less time and cost. You can find the details in this following video.

YouTube Preview Image[by McGovern Institute for Brain Research at MIT]

Nature , Science and many major media have unanimously deemed CRISPRs to be a revolution. Radiolab has discussed its ethical controversies as if the realization of the technology is right around the corner. It has been portrayed as such a simple and approachable method that people even claim to provide CRISPR DIY kit for experiments at home.

However, I think despite these attentions,  the reality is that we are still far from ready to harness CRISPRs. Although many researches has already been using it to edit genes in a variety of bacterias, plants, and animals within a short 3-year period, few studies focused on the limitations and functions of CRISPR itself. Some research was done too early without waiting for the technology to mature, such as the research using human embryos, which has resulted in a less satisfactory result. Some researchers commented that CRISPR can be less accurate than expected and may not be the most efficient and cost-effective solution for certain problems on Quora. Scientist Konstantin Severinov on Quanta Magazine also pointed out that it is still unknown whether defending invaders is the major usage of CRISPRs since many of these spacers appear to be genes of viruses that are long gone. It might be a good time now to slow down and maybe build the technique from ground up concretely first.

by Sainan Liu

The Never-Ending Winter: The Snowball Earth Hypothesis

The history of the planet Earth will always be a mystery that many geologists strive to figure out. In one of my earth and ocean science courses this semester, we talked about the possibility of a Snowball Earth. When I first heard the name, Snowball Earth, I was confused as to what a snowball earth is and why scientists call it that but as the professor began explaining the concept, it became clear.

The Snowball Earth Hypothesis suggests that based on the rock record, the Earth was mostly or entirely covered by ice at certain points over a period of billions of years. Throughout most of the continents today, geologists have found dropstones which are a type of glacial deposits that suggest the presence of ice.

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Glacial Dropstone Source: Michael C. Rygel (WIkimedia Commons)

Dropstones are formed when glaciers move across the land and scratching the surface resulting in the collection of rock pieces. These pieces then combine together and are eventually dropped as the ice melts onto land or into the ocean and are eventually covered by sediments and turned to rock. As these dropstones form, the magnetite particles in the stones reflect the direction of the magnetic field. As a result, geologists have concluded that some of these glacial dropstones were formed at the equator.

Although hard to believe that the Earth can be covered in ice, several factors may have enabled the Earth to be cold enough to have ice at the equator. The first factor was that the sun was not emitting as much energy in the past and therefore the Earth was receiving less heat. Secondly, due to intense rainfall, the CO2 in the atmosphere are drawn down by the rain due to chemical weathering leading to a drop in temperatures.

Quelccaya_Glacier

Quelccaya Glacier Source: Edubucher (Wikimedia Commons)

As temperatures drop, the polar ice caps start advancing towards the equator. As the amount of ice increases, the albedo effect becomes stronger leading to lower temperatures. At this point, I was thinking, how does this make sense since we are not living in igloos today? Well, the answer to that are volcanoes.

Mahameru-volcano

Mahameru Volcano Source: Jurema Oliveira (Wikimedia Commons)

Due to the heat generated by the magma, volcanoes are able to melt through the ice and release many types of gases into the atmosphere such as CO2 and methane. These gases are important because they trapped heat and led to the end of the Snowball Earth. Therefore, over millions of years, these gases accumulated and eventually, the planet was hot enough to melt the ice within thousands of years.

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Source: Big History Project (Youtube Creative Commons)

Although not all scientists believe in the Snowball Earth, I found this theory to be a good example of what science is about. By looking at rocks underneath the ground and with the knowledge about how certain types of rocks form, geologists were able to hypothesize such an extreme event that occurred before humans walked the planet.

Adrian Li